DNA and RNA Structure and Replication

DNA Review

• DNA and RNA consist of unbranched polymers made of repeating nucleotide monomers.
• Nucleotides contain a nitrogenous base, a pentose sugar, and one or more phosphate groups.
• RNA is a single-stranded structure.
• DNA is a double helix structure.

List of Nitrogenous Bonds

• Purines include Adenine and Guanine.
• Pyrimidines include Cytosine, Thymine, and Uracil.
• A repeating sugar-phosphate-sugar pattern forms the backbone, with bases hanging off as appendages.
• Phosphodiester bonds link the 5' carbon of one nucleotide to the 3' carbon of another.
• Hydrogen bonds, which are easily destructed, connect nitrogenous bases.

Chargaff's Rule

• In DNA, Adenine pairs with Thymine (A=T, T=A).
• In DNA/RNA, Guanine pairs with Cytosine (G=C, C=G).
• In RNA, Adenine pairs with Uracil (A=U, U=A).

DNA Replication

• Base pairing is central to replicating a template strand.
• Complementary DNA strands act as templates for building new strands during replication.
• During DNA replication, the parent molecule separates with the help of the Helicase protein, forming a daughter strand.
• Helicase is responsible for unzipping the DNA strand.
• When a double helix replicates, each daughter molecule has one old strand and one newly made strand.

Steps of DNA Replication

• Begins at the double helix.
• Single-strand binding proteins ensure strand stability.
• Topoisomerase reduces overwinding by breaking and rejoining DNA strands.
• An RNA primer, made of primase, starts nucleotide base addition.
• Prokaryotes have 1 origin of replication.
• Eukaryotes have one or more origins of replication.
• The leading strand is continuous.
• The lagging strand is fragmented, requiring constant initiation.
• DNA Polymerase III adds nucleotides only to the free 3' end of a growing strand, elongating in the 5' to 3' direction.
• DNA Polymerase I replaces RNA primers.
• DNA Ligase glues the strand back together.
• Okazaki fragments create gaps on the strand
• DNA replication BIDIRECTIONAL
• Enzymes remove telomeres which leads to shorter strands.
• Nucleases proofread and fix mismatched base pairs.

Transcription and Translation of Genes

Overview

• Central Dogma: DNA -> RNA -> Protein Transcription: RNA acts as a bridge between genes and proteins by copying information from DNA and synthesizing it into RNA within the nucleus. Translation: This uses mRNA to synthesize polypeptide chains from RNA to protein with ribosomes at the site of translation
• Messenger RNA (mRNA) carries transcribed information from DNA.
• Ribosomal RNA (rRNA) is where polypeptide chains are built to enable translation
• Transfer RNA (tRNA) delivers amino acids to the ribosome.

Transcription

• Enzymes use a gene's nucleotide sequence to create a complementary RNA strand.
• RNA polymerase catalyzes RNA synthesis by separating DNA strands and joining RNA nucleotides.
• RNA synthesis follows DNA base-pairing rules, substituting uracil for thymine.
• RNA Polymerase II separates and unwinds the double helix and makes and base pairs mRNA.

Process of Transcription

• Initiation: RNA polymerase II binds and initiates transcription. RNA Polymerase II, Transcription Factors, and Promoter form a Transcription Initiation Complex.
• A promoter region is where transcription starts when RNA polymerase attaches.
• A transcription unit is a stretch of DNA that is transcribed.
• Transcription factors guide RNA polymerase II.
• Elongation: RNA polymerase II unwinds the DNA helix to create new RNA.
• RNA polymerase adds nucleotides to the 3' end of the growing RNA molecule as moves along the DNA, untwisting the double helix 10-20 bases at a time.
• The newly synthesized RNA molecule separates from its DNA template.
• Termination: RNA polymerase II transcribes a (AAUAAA) "Polyadenylation signal", which signals protein to cut the RNA transcript from polymerase.
• After copying, completed RNA is altered from DNA.
• Enzymes in the eukaryotic nucleus modify pre-mRNA before it is dispatched to the cytoplasm.
• mRNA end alteration occurs distinctly at each end of a pre-mRNA molecule
• The 5' end receives a modified nucleotide 5' cap.
• The 3' end receives a poly-A tail (PolyAdenine Tail).
• A mRNA molecule with a continuous coding sequence is created by removing exons from RNA and splicing others together in various combinations.
• Spliceosomes cut out introns leaving only exons coding segments to form mRNA
• 5' cup + Poly-A Tail + Exons result in mRNA

Translation

• An mRNA's genetic information is converted into a new polypeptide chain (amino acid).
• RNA transcript determines the sequence of Amino Acids.
• Codons are triplets of three ordered nitrogenous bases where each letter equates to one codon and each codon equates to one amino acid making gene to protein based on a triplet code
• Amino acids are linked together into a chain.

Process of Translation

• Initiation: A Translation complex is completed
• Requires a small ribosomal subunit, methionine, and a large ribosomal subunit with start codon (AUG)
• Elongation: Begins before the codon AUG called start codon.
• tRNA carries amino acids to the Acceptance Site where it enters and moves to the Processing Site to creates a new peptide formation then leaves the Exit Site
• Termination: Reaches one of three stop codons which ends complex dissociation
• Stop Codons: (UAA, UAG, UGA)
• Structure: The primary protein structure is its sequence of amino acids where mRNA determines the sequence

Genetic Engineering

• Biotechnology utilizes biological processes, organisms, or systems to improve the quality of human life.
• Genetic engineering enables direct manipulation of genes within DNA through the alteration of DNA sequenceR.
• Recombinant DNA combines one or more segments into another DNA segment using plasmids found in bacteria/prokaryotic and injects in Eukaryotic cells.

Classical Breeding V.S. Modern Genetic Techniques

• Classical breeding focuses on selected mating of mating of organisms with the mating of organisms with desirable qualities which takes time due to randomness.
• Modern genetic techniques manipulate the genes in order to insert desirable traits with objectives to; introduce new traits, increasing a trait, or disrupting the inhibition of a gene.

Steps in DNA Recombination

• Step 1: Identify a trait of interest.
• Step 2: Isolate the genetic trait of interest.
• Step 3: Select an appropriate vector molecules (genes) that carry DNA to another organism, like plasmids that carry genes for antibiotic resistance needed for survival, making them good for genetic modification.
• Step 4: Gene Modification.
• Cut the desired gene using restriction enzymes.
• Select an appropriate vector to propagate the gene.
• Ligation the desired gene and the vector's gene.
• Transform the gene to the vector for reproduction.
• Select vectors with the new gene and Sequence the to ensure proper product using restriction enzymes

Introducing Desired Genes to Host Organisms

• Methods include chemical (lipofection, calcium chloride), physical (electroporation, microinjection, biolistics), and vectors (Agrobacterium tumefaciens, tobacco mosaic virus)
• Lipofection: insertion of DNA into lipid (endocytosis) for delivery to host cells.
• Electroporation: use electrical pulses to create pores in cells.
• Microinjection: inject with small injection
• Calcium Chloride: using chemicals to transfect a mature cell by treating it with warm and cool baths help dna get in place
• Biolistics: bullet - which used microparticles of gold or tungsten coated with the desired DNA sequence.
• Plasmids as Vectors: genes that are resistant to antibiotics that act as markers to identify cells with recombinant DNA

Human and Chemical Production

• E.coli and Yeast are used for use of use of e coli bacteria (humulin) and yeast (novolin) to produce Humulin and Novolin
• Genetically engineered Bt-endotoxin kills pests when ingested and is not toxic to and is safe for humans.

Evolution

Evolution: The Origin of Species

• Evolution FAQs: only fact is That all living organisms share a common ancestor while other FAQs are fictitious.

Concepts For Evolution

• Evolution is genetic change in a population over multiple generations.
• A population is interbreeding members of the same species.
• Alleles are two or more alternative forms of a gene at the same chromosome location.
• Allele Frequency Is the copy number of an allele divided by the total alleles for that particular gene within the population.
• Macroevolution is large scale evolutionary events, such as the appearance of new species
• Microevolution is Small, generation by generation changes to populations' gene pool
• Charles Darwin is known as the "Father of Evolution"
• Evolution is a genetic population change over multiple generations.
• Descent with modification is the process by which traits are inherited and altered from generation to generation.
• Changes in allele frequencies can be detected by examining it's population.
• A change in allele frequencies determines if a trait would be common.
• Evolution occurs in population

Development of Evolutionary Thought

• Major contributors include Aristotle, Buffon, Lamarck, Lyell, Darwin, and Wallace.
• In 1931, HMS Beagle spent 5 weeks in the Galapagos Islands to gather Charles Darwin's evidence of evolution.

Patterns of Descent with Modification

• All life shares a common Earth-an ancestral organism shared by two or more descent lineages that allowed modification.
• Offspring inherit altered traits.
• Environmental changes would eliminate the more poorly equipped variants, and gradually, the population would change.

Origins of Evolutionary Thought

• Contributors include Hutton, Malthus, Lamarck, Darwin, and Wallace.
• Wallace wrote to Darwin about evolution.

Concept of Natural Selection

• A fundamental mechanism of evolution proposed by Charles Darwin and Aldred Russel Wallace is that
• Organisms with advantageous traits for survival and reproduction are more likely too pass on their genes to the next generation that vice versa, with those of less advantageous traits are less likely to do so.
• Natural selection is a term to describe “this preservation of favorable variations and the rejection of injurious variations.
• Artificial selection : selective breeding according to Darwin is where a human chooses one or a few desired traits, then allows only the individuals that best express those qualities to reproduce.

Requirements for Natural Selection

• Variation: variation in traits such genetic, behavioral, or phenotypic
• Heredity: traits are passed from one generation to the next
• Differential Survival and Reproduction: Nature exerts selective pressures, favoring certain traits.
• Selective pressure: environmental factors
• Time: a slow process

Natural Selection

• Natural Selection is the most important mechanism of evolution which leads to reproduction of an organism.
• Survival of the Fittest: reproductive success across multiple generations.

Modes of Natural Selection

• Directional Selection- favors one extreme phenotype for evolution.
• Disruptive Selection - Evolution of two or more extreme phenotypes .
• Stabilizing Selection - Evolution to favor average traits in a population.

Other Mechanisms of Evolution

• Mutations: changes in an organism's introduces a new allele to the mutation and natural selection acts.
• Gene flow: the movement of individuals in or out of a population.
• Non-random mating: occurs when individuals preferentially mate with specific traits while there is Assortative Mating is mating with similar traits and Disassortative Mating is with different traits.
• Genetic Drift: is the change of allele frequencies occurs mainly by chance where Founder and Bottleneck affects happen.
• The founder effect is a small group leaving and Bottleneck effect is the rapid drop of population

Evidences of Evolution

• Fossils - are remnants, impressions, or traces of prehistoric organisms.
• Body Fossil: remains of an actual organisms which includes bones and such
• Trace Fossil: fossilized imprint of an organisms (including nests or eggs
• Mold Fossil: fossilized impression of the actual organism into the surface
• Relative dating places the fossil to predict age
• Radiometric dating-uses radioactive isotopes to predict time
• Plate Tectonics and Biogeographical locations are plate shift occur
• The anatomical comparisons can be homologous and vestigial 3.1 Homologous - if the similarities between them are same 3.2 Vestigial structure - structure has no function in one species but function in another
• Embryonic Development: physical traits with the processes that produce those traits
• Molecular Comparisons -Utilize DNA sequencing for evolutionary relationship

Taxonomy & Phylogenetics

• Taxonomy is the discipline of identying and classifying with classification and Nomenclature.
• Systematics is the study of evolutionary relationships and the diversification of species with Taxonomy + Phylogeny.

History of Classfication

• Aristotle divided into plant or animal by Habitat
• Carolus Linnaeus identified Scientific Names: composed of two latin terms: a GENUS and a SPECIES
• The first letter of the genus name should be written in CAPITAL LETTERS and the species should be written in all SMALL LETTERS. If the scientific name is computerized, it should be written in italics and underlined when handwritten when the scientific name has already appeared.

Evolution and Classfication

• Descent with modification is modifications
• Tree branching organizes organisms by using catergories.
• Carl Woese introduced the three-domain system.

Example of Taxonomic Hierarchy (From broadest to narrowed/specific)

• Domain - Eukaryote
• Kingdom - Animalia
• Phylum - Chordata
• Class - Mammalia
• Order: Carnivora
• Family: Felidae
• Genus: Panthera
• Species: Panthera Leo
• ΤΑΧΟΝΟMY OF A: Lion